SourceTree - Loses changes and remotes

I have been using SourceTree for many months, and recently I installed manual git msys for bower. Then I had all sorts of problems and abandoned bower usage and uninstalled git.

I reinstalled SourceTree several times.

The problem is that SourceTree acts normally when I first boot up the PC. It shows me my remotes, and shows me my changes. Just as I always expect.

However, after an unknown time (and often instantly, on first launch) it appears to lose all connection to data. This screenshot shows that all my remotes are gone, and that all changes are being ignored.